Whew Matt! I have just printed out your information and will put it together so I can get a clear picture. Quickly,you are correct in thinking that pullups and other lat work will use up some of your energy and your bench total will suffer on that same day's workout. With that said you are looking for real problems with your shoulders if you are not maintaining a balance of tension between the back and chest. If your rhomboids are truly overdeveloped you could be realizing some restrictions of your triceps in their secondary role to your chest work. You could benefit by some tricep work with a focus on function. The extrodinary strength of your rhomboids on the inside of the scapula relative to the connection of your tricep on the outside of your scapula and then the participation of the rotator cuff muscles could be inhibiting your access to the greatest contractile ability of your pecs. Sounds like you have a lot of material so take a look at this. I know you are on a large muscle/compound program but sometimes you need to isolate your attention to these important secondary muscles and the alignment of the whole body.
Abs should be worked like any other muscle. Three days a week with a strong program should be sufficient since, as you already noticed the abs are getting a lot of work in your other body part exercises. Your abs will naturally thicken with the heavy squat, it is a consequence of keeping your upper body from collapsing under the appropriate weight to overload your legs.
Let me study the material you gave me and I'll respond with a more specif response. You are going to pay a price in your energy when you train this heavy. As you continue training you will become more efficient at creating energy and healing. Remember more rest might be necessary, 8-9 hours a night is not uncommon. You will also become more mentally tough and your golgi tendon will develop more tenacity. But as long as you are training at the height of your strength threshhold you will be taxing your energy reserves and also your bodies requirements for food and recovery.
Finally I will remind us all that the body is adaptive to any consisent information. Changing up your workout is one of the best ways to break through your plateau's. More on this when I study all this information. I can't wait to read your othr thread as well. I deal with lots of back problems and love that you are championing the cause of self diligence, self study, and self healing! Later